Obtaining alignment from psiblast

Question

[nilus1432]

Hi everyone,

I am using stand alone version of Psi-blast.

I want to get just the query sequence followed by matched-hit sequences (both aligned) in fasta format.

How to do it in Biopython or stand alone blast.

1. Some posts suggest Mview: for some reason this solution I am not using

2. I can get qseq and sseq using -outfmt 6 option but not full sequences in aligned format.

3. Similar to 2 I am able to get with biopython but again not full aligned sequences as I need

Thanks for help

-nil

Answer 1

[a.polo88]

perhaps :

in Ubuntu/Debian NCBI tools available by installing the package blast2 (or the newest ncbi-blast+) (sudo) apt-get install blast2 or (sudo) apt-get install ncbi-blast+ another useful tool is formatdb

For blast2 users!

formatdb -i <db_fasta_file>

For blast+ users (on Linux or Windows)

makeblastdb -in <db_fasta_file> -dbtype prot

[nilus1432]

I already have local blast, I want formatted output, any ideas?

[a.polo88]

an example perhaps of formatted output can be:

psiblast -query CCL25_HUMAN.fa -db UniprotKBSP.fa -evalue 0.0001 -num_iterations 3 -out_ascii_pssm CCL25_HUMAN.pssm -out CCL25_HUMAN.alns.blast

where :

Input sequence: CCL25_HUMAN.fa
Search database: UniprotKB/SwissProt (UniprotKBSP.fa)
E‐value threshold: 0.0001
Output file for pairwise alignments: CCL25_HUMAN.alns.blast
Output file for PSSM/Profile matrices: CCL25_HUMAN.pssm
Three iterations (-‐j 3)

if you ask for this, otherwise you can see other parameters simple with the help() command if you use one of these programs.

Answer 2

[Siva]

I don't think there is any option in PSI-BLAST to output the multiple alignment.

I remember buildali.pl of HHsuite used to have an option to extract the multiple alignment in FASTA format from PSI-BLAST result. It now uses CS-BLAST instead of PSI-BLAST. However, I found a version of buildali.pl (probably an older version) whose description says that it extracts multiple alignment from PSI-BLAST result.

There is also another tool called Blammer from HHsuite that converts BLAST/PSI-BLAST result in to multiple alignments.

[nilus1432]

Yes, this is what I am looking for. I tried buildali.pl on the psiblast output (version 2.2.30) which was run using psiblast -query fasta -db database -num_iterations=3 -out out.align.

However, the buildali.pl terminates with a error

Error in alignhits.pl: blast output file out.align truncated:

Any suggestions??

Thanks